4DGT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PLP-BOUND PUTATIVE AMINOTRANSFERASE FROM CLOSTRIDIUM DIFFICILE 630 CRYSTALLIZED WITH MAGNESIUM FORMATE

Authors :   I. G. Shabalin, O. Onopriyenko, M. Kudritska, M. Chruszcz, S. Grimshaw P. J. Porebski, D. R. Cooper, A. Savchenko, W. F. Anderson, W. Minor, Ce Structural Genomics Of Infectious Diseases (Csgid)

Date :   26 Jan 12 (Deposition) - 08 Feb 12 (Release) - 08 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (1x),B (1x)

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Internal Aldimine With Pyridoxalphosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. G. Shabalin, O. Onopriyenko, M. Kudritska, S. Grimshaw, M. Chruszcz, P. J. Porebski, D. R. Cooper, A. Savchenko, W. F. Anderson W. Minor
Crystal Structures Of Putative Aminotransferase From Clostridium Difficile 630
To Be Published
PubMed: search

Molecule 1 - PUTATIVE PYRIDOXAL PHOSPHATE-DEPENDENT TRANSFERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIPL
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	CD2733, CD630_27330
	Organism Scientific	:	CLOSTRIDIUM DIFFICILE
	Organism Taxid	:	272563
	Strain	:	630

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	MG	9	Ligand/Ion	MAGNESIUM ION
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:95 , VAL A:96 , ILE A:97 , PRO A:98 , TYR A:121 , CYS A:168 , ASN A:172 , ASP A:200 , ILE A:202 , HIS A:203 , LYS A:235 , HOH A:566 , HOH A:712 , HOH A:862 , HOH A:879 , HOH A:916 , TYR B:62 , HOH B:603	BINDING SITE FOR RESIDUE PLP A 401
02	AC2	SOFTWARE	PRO A:312 , HOH A:645 , HOH A:651 , HOH A:752 , HOH A:841 , HOH A:873	BINDING SITE FOR RESIDUE MG A 402
03	AC3	SOFTWARE	SER A:218 , HOH A:691 , HOH A:699 , HOH A:775 , HOH A:823 , HOH A:824	BINDING SITE FOR RESIDUE MG A 403
04	AC4	SOFTWARE	HOH A:680 , HOH A:781 , HOH A:784 , HOH A:869 , HOH A:900	BINDING SITE FOR RESIDUE MG A 404
05	AC5	SOFTWARE	ASN A:145 , ASN A:147 , ASN B:145 , ASN B:147	BINDING SITE FOR RESIDUE CL A 405
06	AC6	SOFTWARE	MET A:311 , PRO A:312 , LYS A:313 , HOH A:620 , HOH A:759	BINDING SITE FOR RESIDUE CL A 406
07	AC7	SOFTWARE	GLU A:222 , HOH A:664 , HOH A:767 , HOH A:769 , HOH A:855 , HOH A:856	BINDING SITE FOR RESIDUE MG A 407
08	AC8	SOFTWARE	TYR A:62 , ASP A:266 , GLY B:95 , VAL B:96 , ILE B:97 , PRO B:98 , TYR B:121 , CYS B:168 , ASN B:172 , ASP B:200 , ILE B:202 , HIS B:203 , LYS B:235 , HOH B:616 , HOH B:618 , HOH B:648 , HOH B:658	BINDING SITE FOR RESIDUE PLP B 401
09	AC9	SOFTWARE	PRO B:312 , HOH B:629 , HOH B:801 , HOH B:869 , HOH B:876 , HOH B:880	BINDING SITE FOR RESIDUE MG B 402
10	BC1	SOFTWARE	HOH B:532 , HOH B:783 , HOH B:784 , HOH B:785 , HOH B:878 , HOH B:904	BINDING SITE FOR RESIDUE MG B 403
11	BC2	SOFTWARE	MET B:311 , PRO B:312 , LYS B:313 , HOH B:745 , HOH B:827	BINDING SITE FOR RESIDUE CL B 404
12	BC3	SOFTWARE	THR A:179 , ASP A:181 , LYS B:315 , HOH B:905	BINDING SITE FOR RESIDUE CL B 405
13	BC4	SOFTWARE	HOH B:646 , HOH B:711 , HOH B:763 , HOH B:764	BINDING SITE FOR RESIDUE MG B 406
14	BC5	SOFTWARE	LYS B:160 , HIS B:193 , HOH B:675 , HOH B:707 , HOH B:758 , HOH B:835 , HOH B:938	BINDING SITE FOR RESIDUE MG B 407
15	BC6	SOFTWARE	HOH B:660 , HOH B:695 , HOH B:848 , HOH B:854 , HOH B:893 , HOH B:897	BINDING SITE FOR RESIDUE MG B 408

(no "SS Bond" information available for 4DGT)

Asymmetric Unit

No.	Residues
1	Glu A:118	-	Pro A:119
2	Asn A:169	-	Pro A:170
3	Asn A:172	-	Pro A:173
4	Glu B:118	-	Pro B:119
5	Asn B:169	-	Pro B:170
6	Asn B:172	-	Pro B:173

(no "SAP(SNP)/Variant" information available for 4DGT)

(no "PROSITE Motif" information available for 4DGT)

(no "Exon" information available for 4DGT)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:387
 aligned with Q183G9_PEPD6 | Q183G9 from UniProtKB/TrEMBL  Length:388

    Alignment length:387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       
         Q183G9_PEPD6     2 NYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSLKNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAISLLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMDYEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPDEKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNIDFAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVALNQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN 388
               SCOP domains d4dgta_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhh....ee..........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhh....eeee.....hhhhhhhhhh..eeee...ee.....ee.hhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh..eeeee..............hhhhhhhhhhhheeeee.hhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee.hhhh.hhhhhhhhhhhh..ee.ee.hhhh.....eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dgt A   2 NYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSLKNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAISLLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMDYEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPDEKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNIDFAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVALNQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN 388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with Q183G9_PEPD6 | Q183G9 from UniProtKB/TrEMBL  Length:388

    Alignment length:387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       
         Q183G9_PEPD6     2 NYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSLKNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAISLLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMDYEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPDEKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNIDFAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVALNQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN 388
               SCOP domains d4dgtb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhh....ee..........hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhh....eeee.....hhhhhhhhhh..eeee...ee.....ee.hhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh..eeeee..............hhhhhhhhhhhheeeee.hhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee.hhhh.hhhhhhhhhhhh..ee.ee.hhhh.....eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dgt B   2 NYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSLKNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAISLLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMDYEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPDEKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNIDFAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVALNQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN 388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: automated matches (163)

Protein domain: automated matches (163)

Clostridium difficile [TaxId: 272563] (2)

1a	d4dgta_	A:
1b	d4dgtb_	B:

(no "CATH Domain" information available for 4DGT)

(no "Pfam Domain" information available for 4DGT)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q183G9_PEPD6 | Q183G9)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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	Cis Peptide Bonds
		Asn A:169 - Pro A:170	[ RasMol ]
		Asn A:172 - Pro A:173	[ RasMol ]
		Asn B:169 - Pro B:170	[ RasMol ]
		Asn B:172 - Pro B:173	[ RasMol ]
		Glu A:118 - Pro A:119	[ RasMol ]
		Glu B:118 - Pro B:119	[ RasMol ]

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	4dgt
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Description

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Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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